Biol Lecture Study Guide Exam 2 PDF

Based on the detailed information provided from the lecture "2.1 Viruses and the Origins of Life on Earth," here are the responses to your questions: 1. Describe how viruses were first discovered: Viruses were known to exist before they could be seen. In 1884, a porcelain filter was developed that c...

Based on the detailed information provided from the lecture "2.1 Viruses and the Origins of Life on Earth," here are the responses to your questions: 1. Describe how viruses were first discovered: Viruses were known to exist before they could be seen. In 1884, a porcelain filter was developed that could remove bacteria. In 1886, tobacco mosaic disease was shown to be infectious. In 1892, it was discovered that the disease could still be transmitted even after the infectious agent had been filtered, suggesting that something smaller than bacteria was responsible. The tobacco mosaic virus was the first virus to be discovered. 2. Explain the three hypotheses about how viruses evolved: Regressive Hypothesis: Viruses may have devolved from free-living cells, losing non-essential functions as they adapted to a parasitic lifestyle. Progressive Hypothesis: Viruses could have originated from nucleic acid fragments that escaped from the genetic material of larger organisms. Virus-First Hypothesis: Viruses may represent the first self-replicating units, predating modern cells. There is currently no significant evidence to conclusively support any of these hypotheses. 3. Describe the structure of a virus: A virus, or virion, typically has a nucleic acid core containing either DNA or RNA, which can be double-stranded or single-stranded. This genetic material is protected by a protein capsid, and most viruses have glycoproteins to help them attach to host cells. Some viruses have an outer envelope and may also carry additional proteins, like enzymes. 4. Recognize the basic shapes of viruses: The basic shapes of viruses include helical, icosahedral, and complex structures like head-tail or “blob” configurations. 5. List the steps of a viral infection and explain what occurs at each step: 1. Attachment: The virus binds to specific receptor molecules on the host cell. 2. Entry: The viral genome enters the host cell via injection, fusion, or endocytosis. 3. Replication: The host cell synthesizes viral proteins and genomes. 4. Assembly: New virions are assembled inside the host cell. 5. Release/Egress: Virions are released from the host cell through lysis, budding, or exocytosis. 6. Compare and contrast the lytic and lysogenic cycles of bacteriophage replication: Lytic Cycle: The bacteriophage infects the bacterium, uses the bacterium’s machinery to replicate, and then lysis (destruction) of the host cell occurs to release new phages. Lysogenic Cycle: The bacteriophage integrates its DNA into the bacterial chromosome, where it can be dormant and replicated with the host cell’s DNA before possibly entering the lytic cycle later. 7. Contrast the transmission of plant and animal viruses: Plant Viruses: Transmission usually requires a vector or damaged tissue due to the cell wall barrier; they can be transmitted horizontally (between individuals) or vertically (from parent to offspring). Animal Viruses: Transmission can occur via various routes such as respiratory droplets, physical contact, or vectors; they can cause acute, chronic, or latent infections and may lead to diseases or be asymptomatic. 8. Describe latent and oncogenic viral infections and identify examples of each: Latent Infections: The virus remains dormant within the host for a period of time and can reactivate later. An example is herpes simplex virus, which can remain in nerve tissue and reactivate. Oncogenic Infections: Viruses that can lead to cancer. An example is human papillomavirus (HPV), which can lead to cervical cancer. 9. Compare vaccinations and anti-viral drugs as medical approaches to viruses: Vaccinations: Prepared using attenuated or killed viruses or molecular subunits to trigger an immune response, preventing infection. Antiviral Drugs: Target different phases of the viral life cycle to inhibit virus replication and spread, such as Tamiflu or anti-HIV drugs (HAART). 10. Describe prions and their basic properties: Prions are infectious particles made solely of proteins without any nucleic acid. They cause fatal neurodegenerative diseases, such as Mad Cow Disease and Creutzfeldt-Jakob disease, and are resistant to destruction by cooking. 11. Define viroids and their targets of infection: Viroids are small circles of RNA without a protein capsid or envelope. They only infect plants and replicate using the host cell machinery without producing proteins. 12. Describe the four hypotheses on the origin of organic molecules on Earth: Hypothesis 1: Organic molecules formed from inorganic compounds in the atmosphere (Oparin-Haldane Hypothesis). Hypothesis 2: Organic molecules came from outer space via comets and meteorites. Hypothesis 3: Organic molecules synthesized at hydrothermal vents on the ocean floor. Hypothesis 4: Organic molecules formed upon impact from meteorites, facilitated by clay surfaces. 13. Explain the different problems to solve, and scientific hypotheses, on the origins of life: Problem 1: The origin of life's organic molecules. Problem 2: Assembly of macromolecules from monomers. Problem 3: Reproduction of macromolecules. Problem 4: Assembly of macromolecules into a system separate from their environment. 14. Explain the importance of the discovery of ribozymes: The discovery of ribozymes supported the RNA World hypothesis, demonstrating that RNA molecules could act both as carriers of genetic information and as catalysts for their own replication, suggesting a possible early form of life before DNA and proteins. Based on the provided lecture notes on "2.2 Prokaryotes," here are the answers to your questions: 15. Define each type of extremophile: Acidophiles: Thrive in acidic environments with a pH of 3 or below. Alkaliphiles: Prefer highly alkaline environments with a pH of 9 or higher. Thermophiles: Live in hot temperatures ranging from 60-80°C (140-176°F). Hyperthermophiles: Can survive in extremely hot environments with temperatures between 80-122°C (176-250°F). Psychrophiles: Prefer cold temperatures ranging from -15 to 10°C (5-50°F) or lower. Halophiles: Thrive in high salt concentrations of at least 0.2 M. Osmophiles: Live in environments with high sugar concentrations. Hypoliths: Survive in areas with low humidity/water availability. 16. Describe the basic structure of a typical prokaryotic cell: Plasma Membrane: Encloses the cell, regulating the passage of substances in and out. Cytoplasm: Jelly-like substance within the cell containing all organelles and cell parts. DNA: Single, circular, double-stranded chromosome located in the nucleoid. Ribosomes: Synthesize proteins. 17. Identify some differences in structure between Archaea and Bacteria: Plasma Membrane: Archaea have branched hydrocarbon chains attached to glycerol by ether bonds, whereas bacteria have unbranched chains attached by ester bonds. Cell Wall: Archaeal cell walls are composed of polysaccharides, while bacterial cell walls contain peptidoglycan. Gene Expression: Archaeal mechanisms are more similar to eukaryotes, with similar enzymes for transcription and translation. 18. Explain reproduction in prokaryotes: Prokaryotes reproduce asexually through binary fission, where the DNA is replicated, and the cell divides into two genetically identical cells. 19. Describe the methods of horizontal gene transfer in prokaryotes: Transformation: Uptake of DNA from the environment. Transduction: Transfer of DNA from one cell to another via bacteriophages. Conjugation: Direct transfer of DNA between cells through a pilus. 20. Identify the macronutrients & micronutrients needed by prokaryotes, and explain their importance: Macronutrients (CHNOPS): Essential for building macromolecules; carbon for organic compounds, nitrogen for proteins and nucleic acids, etc. Micronutrients (metallic elements like iron, boron, manganese): Serve as cofactors for enzymes and are crucial for various cellular processes. 21. Describe the ways in which prokaryotes get energy and carbon for life processes: Photolithoautotrophs: Use sunlight for energy and CO2 as a carbon source. Chemoorganotrophs: Obtain energy and carbon from organic compounds. Chemolithoautotrophs: Obtain energy from inorganic compounds and carbon from CO2. 22. Define the terms obligate aerobes, obligate anaerobes, and facultative anaerobes: Obligate Aerobes: Require oxygen to survive. Obligate Anaerobes: Cannot survive in the presence of oxygen. Facultative Anaerobes: Can survive with or without oxygen. 23. Compare gram-positive & gram-negative bacteria: Gram-Positive Bacteria: Have a thick peptidoglycan layer in their cell wall and stain purple with Gram staining. **Gram -Negative Bacteria:** Have a thin peptidoglycan layer but possess an outer membrane, and they stain pink or red with Gram staining. 24. Describe the roles of prokaryotes in the carbon and nitrogen cycles: Carbon Cycle: Prokaryotes participate as producers (photosynthetic bacteria fix carbon into sugars), consumers (using organic compounds and releasing CO2), and decomposers (making organic molecules from dead organisms available). Nitrogen Cycle: They are involved in nitrogen fixation (converting atmospheric N2 into ammonia), ammonification (release of ammonia during decomposition), and nitrification (conversion of ammonia into nitrates). 25. Explain why natural reservoirs make disease eradication difficult: Natural reservoirs (populations of organisms that harbor pathogens) make disease eradication challenging because they maintain the pathogen within the environment, enabling continued transmission to the target population. 26. Describe the link between biofilms and diseases: Biofilms are microbial communities that are difficult to destroy and can cause diseases by adhering to surfaces, like medical devices in hospitals, and becoming resistant to drugs. 27. Explain how overuse of antibiotics may be creating “super bugs”: The overuse and misuse of antibiotics, such as in livestock farming and treating viral infections, can lead to antibiotic resistance, where bacteria evolve mechanisms to survive exposure to antibiotics, creating "super bugs." 28. Explain the importance of MRSA with respect to the problems of antibiotic resistance: MRSA (Methicillin-resistant Staphylococcus aureus) is significant because it is resistant to many antibiotics, including methicillin, making it a prime example of the challenges posed by antibiotic-resistant bacteria, especially in healthcare settings. 29. Describe the beneficial effects of bacteria that colonize our skin and digestive tracts: The bacteria that colonize our skin and digestive tracts play essential roles in digestion, protecting against pathogens, producing vitamins, and may influence our mood, energy levels, and weight. They also contribute to the development of our immune system and help in the metabolism of foods that the human body cannot digest on its own. 2.3 Eukaryotic Cells and Protists 30. List the unifying characteristics of eukaryotes: Cells with nuclei surrounded by a nuclear envelope Presence of mitochondria Cytoskeleton for structure and transport Flagella or cilia in some cells Linear chromosomes organized with histones Division by mitosis Capability for sexual reproduction and meiosis Many have cell walls 31. Describe what scientists know about the origins of eukaryotes based on the last common ancestor: Scientists believe all living eukaryotes are descendants of a single common ancestor that likely had a nucleus, mitochondria, a cytoskeleton, and the ability to reproduce sexually. This ancestor appeared after the earliest prokaryotes and may have originated through processes like membrane proliferation and endosymbiosis. 32. Explain the endosymbiotic theory & the evidence that supports the theory: The endosymbiotic theory suggests that eukaryotic cells originated from a symbiotic relationship between an ancestral prokaryote and an aerobic prokaryote, which became the mitochondria. Evidence includes similarities in DNA, ribosomes, and membranes between mitochondria/chloroplasts and bacteria, and the fact that these organelles replicate independently of the cell. 33. Distinguish between primary & secondary endosymbiosis: Primary Endosymbiosis: Occurs when a eukaryote engulfs a prokaryote, which becomes an organelle (e.g., the engulfment of an aerobic bacterium leading to the formation of mitochondria). Secondary Endosymbiosis: Happens when a eukaryote engulfs another eukaryote that has already undergone primary endosymbiosis. 34. Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes: Plants are related to the supergroup Archaeplastida, animals to the supergroup Opisthokonta, and fungi also to Opisthokonta. These relationships are based on genetic analyses, including similarities in RNA and other molecular structures. 35. Describe the metabolic diversity of protists: Protists exhibit a wide range of metabolic pathways. Some are photoautotrophs with chloroplasts, functioning as primary producers, while others are heterotrophs consuming organic material. There are also mixotrophs that can switch between photoautotrophy and heterotrophy. 36. Describe the life cycle diversity of protists: Protists have a variety of life cycles, from simple ones involving asexual reproduction to complex ones with sexual reproduction. Some have alternating phases of sexual and asexual reproduction, and conditions like environmental stress can trigger the switch from one to the other. 37. Describe the different ways protists can reproduce: Protists can reproduce vegetatively through fragmentation, asexually by binary fission, budding, or spores, and sexually through the fusion of gametes. 38. Identify defining features of protists in each of the six supergroups of eukaryotes: The defining features of protists in the six eukaryotic supergroups are varied, including: Archaeplastida: Includes red and green algae, with photosynthetic abilities similar to land plants. Amoebozoa: Characterized by amoebas with lobed pseudopodia. Opisthokonta: Contains organisms like choanoflagellates, with a posterior flagellum. Rhizaria: Known for thin pseudopodia and often shell-like structures. **Chromalveolata:** Diverse group including organisms with complex life cycles like Plasmodium, and important photosynthetic organisms like diatoms. – Excavata: Includes organisms with unique flagella and feeding grooves, some of which are important parasites like Giardia. 39. Describe the role that protists play in the ecosystem: Protists play crucial roles in ecosystems as primary producers, particularly in aquatic environments where they are a major component of plankton. They also function as decomposers, breaking down dead organic material, and as symbionts in various mutualistic relationships. Additionally, protists are important food sources for a variety of organisms, contributing to the food web dynamics. 40. Describe important pathogenic species of protists: Some protists cause significant diseases in humans, such as Plasmodium spp. which causes malaria, and Trypanosoma brucei which leads to African sleeping sickness. In plants, protists like Phytophthora infestans can cause blights, including the one responsible for the Irish potato famine. These pathogenic protists can have a profound impact on human health and agriculture. 2.4 Fungi 41. Identify the kingdom most closely related to fungi and their common ancestor: The kingdom most closely related to fungi is Animalia. Both animals and fungi are more closely related to each other than either is to plants, and they share a common ancestor that was likely a flagellated unicellular protist. 42. Identify and describe the key adaptations and traits unique to fungi: Key traits of fungi include: A cell wall made of chitin A primarily haploid life cycle with a transient diploid stage The formation of spores for reproduction Heterotrophy through external digestion and absorption of nutrients Hyphal growth, which provides a large surface area for nutrient absorption 43. Describe general fungal morphology, life cycle, and metabolic traits: Morphologically, fungi are composed of hyphae that form a network called a mycelium. They reproduce through spores, which can be sexual or asexual. Metabolically, they are heterotrophs that absorb nutrients after externally digesting their food with enzymes. 44. Explain sexual and asexual reproduction in fungi: In sexual reproduction, fungi undergo plasmogamy, karyogamy, and meiosis to produce spores. Asexually, they reproduce by mitosis, forming genetically identical spores, budding, or fragmentation. 45. Identify characteristics that fungi share with plants, animals, and bacteria: With plants: immobility and a cell wall. With animals: heterotrophy and storage of carbohydrates as glycogen. With bacteria: role as decomposers and absorption of nutrients across the cell surface. 46. Describe the mode of nutrition of fungi: Fungi are heterotrophic and absorb nutrients. They secrete digestive enzymes into their surroundings to break down complex organic material into simpler compounds, which are then absorbed through their hyphae. 47. Identify fungi and place them into the five major phyla according to current classification: The five phyla are: Chytridiomycota: Chytrids, the simplest fungi, often aquatic. Glomeromycota: Form arbuscular mycorrhizae with plant roots. Zygomycota: Include molds like Rhizopus. Ascomycota: Sac fungi, include morels and yeasts. Basidiomycota: Club fungi, include mushrooms and puffballs. 48. Describe each phylum in terms of major representative species and patterns of reproduction: Chytridiomycota: Includes simple fungi like chytrids that can reproduce both sexually and asexually. Glomeromycota: Almost exclusively form symbiotic relationships with plants, reproducing asexually. Zygomycota: Known for their zygospores and include species like black bread mold. Ascomycota: Characterized by their production of ascospores within a sac-like ascus and include yeasts and truffles. Basidiomycota: Produce basidiospores on club-like basidia and include mushrooms and toadstools. 49. **Describe the role of fungi in various ecosystems: Fungi play critical roles in ecosystems as decomposers, breaking down dead organic matter and recycling nutrients. They also form symbiotic relationships with plants (mycorrhizae) that enhance nutrient uptake for the plants. In addition, fungi serve as food for many organisms and are essential in mutualistic relationships such as lichens. 50. Explain the mutualistic relationship in lichen: Lichen is a mutualistic association between a fungus, typically an ascomycete, and a photosynthetic partner, usually an alga or cyanobacterium. The fungus provides structure, protection, and water absorption, while the photosynthetic partner supplies carbohydrates through photosynthesis. 51. Describe mutualistic relationships of fungi with plant roots and photosynthetic organisms: In mycorrhizal relationships, fungi colonize plant roots and extend the root's capability to absorb water and nutrients from the soil, while the plant supplies the fungus with carbohydrates formed during photosynthesis. Endophytic fungi live within plant tissues and provide benefits like disease resistance. 52. Explain why antifungal therapy is hampered by the similarity between fungal and animal cells: Fungal cells are eukaryotic, like animal cells, and share many cellular processes and components. Therefore, it's challenging to find targets for antifungal drugs that don't also harm human cells, leading to a narrower therapeutic index and potential side effects. 53. Describe ways humans have benefited from fungi: Humans benefit from fungi in numerous ways, including the use of yeast in fermentation to produce bread, beer, and wine. Fungi are also sources of antibiotics like penicillin, and they play roles in biotechnology, such as in the production of insulin and other pharmaceuticals. Additionally, fungi are used in bioremediation processes to clean up environmental contaminants.